Actually, it wasn't so much of an alternate ending as the original ending, though I did read that Spielberg may have shot two endings at the same time, the unused and the used one. I guess it wouldn't be too much of a spoiler, as it wasn't used, but I'll put it in invisotext anyway:
| Spoiler: |
| In the unused ending, the characters played by Tom Hanks and Catherine Zeta-Jones get together romantically . In the theatrical ending, they don't. |
Frankly, I kind of prefer the original ending as it better fits the romantic and fanciful tone of the movie. I think this was one case where a filmaker felt pressured to use the less happy ending.